CN106096326B - A kind of differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy - Google Patents
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- 230000035772 mutation Effects 0.000 title claims abstract description 15
- 238000000455 protein structure prediction Methods 0.000 title claims abstract description 15
- 238000012360 testing method Methods 0.000 claims abstract description 24
- 230000001174 ascending effect Effects 0.000 claims abstract description 6
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- 238000005070 sampling Methods 0.000 description 1
- 150000003384 small molecules Chemical class 0.000 description 1
- 238000002424 x-ray crystallography Methods 0.000 description 1
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Abstract
A kind of differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy carries out ascending order arrangement, and calculate the average energy error amount of each conformation and minimum energy conformation according to the energy value of each conformation first；Then, the lower conformation of selected part energy calculates barycenter conformation；Finally, judge the search condition that algorithm is reached according to average energy error amount, test conformation is generated to design different barycenter Mutation Strategies, i.e. if average energy error amount is more than the threshold value of setting, DE/rand to centroid/1 strategies are then designed into row variation, the homologous segment in the conformation randomly selected, which is replaced, by the Partial Fragment extracted in barycenter conformation generates test conformation, otherwise DE/centroid/2 strategies are designed into row variation, the homologous segment in barycenter conformation, which is replaced, by the segment extracted in randomly selected conformation generates test conformation, to improve algorithm search efficiency and precision of prediction.
Description
Technical field
The present invention relates to a kind of biological information, intelligent optimization, computer application fields, more particularly to, it is a kind of
Differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy.
Background technology
Nineteen fifty-three, J.Watson and F.Crick are in Britain《Nature》DNA molecular double-spiral structure mould has been delivered on magazine
Type indicates the birth of molecular biology truly；After 5 years, F.Crick proposes molecular biology " central dogma "
Imagine, discloses the universal law of life hereditary information transmission.As the key component of the rule, from DNA to protein amino
The cracking work of three genetic codes (referred to as " first password ") of acid sequence has just been fully completed early in nineteen sixty-five；However,
Code of folding from amino acid sequence to space structure (referred to as " the second password ") not yet cracks so far.With mankind's base in 2003
Because of the completion of group examining order, protein amino acid sequence quantity is increased sharply, and the theoretical research of protein folding password becomes current
A protein engineering field critical issue in the urgent need to address.
Structural genomics measure the three-dimensional structure of protein using laboratory facilities.X-ray crystallography method is so far
Until study protein structure most efficient method, attainable precision to be any other method cannot compare, it
Disadvantage is mainly that the crystal of protein is difficult to cultivate and the period of crystal structure determination is longer.Multi-dimensional nmr method can be straight
It connects and measures the conformation of protein in the solution, but since the requirement to sample is big, purity requirement is high, can only measure at present small
Molecule protein.Generally, protein structure experimental determining method extremely time-intensive, expensive is laborious.
Ab initio prediction method is known as the Holy grail in protein structure prediction field, in view of its important biological significance and asks
The complexity of topic, 2005《Science》Magazine is classified as contemporary scientific circle 100 most challenging problems urgently to be resolved hurrily
One of.Protein ab initio prediction method must take into consideration following two factors：(1) protein structure energy function；(2) conformational space
Searching method.First factor substantially belongs to molecular mechanics problem, primarily to each protein knot can be calculated
The corresponding energy value of structure.Second factor substantially belongs to Global Optimal Problem, right by selecting a kind of suitable optimization method
Conformational space carries out fast search, obtains conformation corresponding with a certain global minima energy.Wherein, protein conformation space optimization
Belong to a kind of NP-Hard problems being difficult to resolve very much.Swarm Evolution class algorithm is the important side for studying Molecular Conformation of Proteins optimization
Method includes mainly differential evolution algorithm (DE), genetic algorithm (GA), particle cluster algorithm (PSO), the not only structure letter of these algorithms
It is single, it is easy to accomplish, and strong robustness, therefore, the global minima energy conformer search being often used in ab initio prediction method.
However group's optimization algorithm belongs to a pseudo-similar random optimization approach, the document in terms of existing protein conformation optimization mainly study how
Another local minimum solution is jumped to from a local minimum solution, the intelligence that a kind of mechanism efficiently uses Swarm Evolution process is not provided
Energy information guiding search, it is relatively low so as to cause efficiency of algorithm.In addition, genetic drift in by selection pressure and random sampling procedure
It influences, all individuals will unavoidably converge to some absorbing state in group.For this kind of optimization problem of protein conformation, the suction
It might not be exactly globally optimal solution to receive state, to influence precision of prediction.
Therefore, it is existing based on the Advances in protein structure prediction of group in terms of search efficiency and precision of prediction there is
Defect needs to improve.
Invention content
In order to overcome the shortcomings of existing Advances in protein structure prediction in terms of search efficiency and precision of prediction, the present invention
By extracting the lower Constellation information of energy, barycenter Mutation Strategy is designed, while being based on segment package technique, propose a kind of search
Efficient, the high differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy of precision of prediction.
The technical solution adopted by the present invention to solve the technical problems is：
A kind of differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy, the optimization method includes following
Step：
1) protein force field model, i.e. energy function E (X) are chosen；
2) list entries information is given；
3) it initializes：Population Size NP is set, factor CR is intersected, maximum iteration generates initial structure by list entries
As populationAnd iterations G=0 is initialized,
In, N representation dimensions,Indicate i-th of conformation CiN-dimensional element；
4) the energy function value E (C of current each conformation of population are calculatedi), i=1,2 ..., N, and according to each in current population
Conformation energy value carries out ascending order arrangement to each conformation；
5) the conformation C of minimum energy in current population is found outbest, and calculate the energy and C of other conformationsbestENERGY E
(Cbest) average energy errorIf iterations G=0, enables δmax=δ；
6) each conformation individual C being directed in populationi, i ∈ { 1,2,3 ..., NP } enable Ctarget=Ci, CtargetIndicate mesh
Conformation individual is marked, the lower Constellation information of energy in current population is extracted, following operation is executed and generates variation conformation Cmutant：
6.1) CT conformation before selection rankingWherein CT=
Rand (NP/3, NP/2), rand (NP/3, NP/2) indicate the random integers between NP/3 and NP/2,Indicate m-th of choosing
Take the N-dimensional element of conformation；
6.2) the barycenter conformation C of CT selected conformation is calculatedcentroid=(xcentroid,1,xcentroid,2,…,
xcentroid,N), wherein conformation CcentroidJth tie up elementJ=1,
2,…,N；
6.3) sequence length L is set, generates 4 integers randint1, randint2, randint3 at random between 1 and L
And randint4, wherein randint1 and randint2, randint3 and randint4 it is different, enable a=min
(randint1, randint2), b=max (randint1, randint2), c=min (randint3, randint4), d=
Max (randint3, randint4), wherein min indicate that the minimum value of two numbers, max is taken to indicate to take the maximum value of two numbers；
If 6.4) 0.5 δ of δ ＞max, then DE/rand-to-centroid/ strategies are designed into row variation：From current population
Randomly select two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction barycenter conformation Ccentroid
Dihedral angle corresponding to amino acid of the position a to the segment of position b replaces conformation Crand1Same position corresponding to dihedral angle,
Extract conformation C simultaneouslyrand2Dihedral angle corresponding to amino acid of the position c to the segment of position d replaces conformation Crand1Same position
Corresponding dihedral angle, then by gained Crand1Segment is carried out to assemble to obtain variation conformation individual Cmutant；
If 6.5) δ of δ≤0.5max, then DE/centroid/2 strategies are designed into row variation：It is selected at random from current population
Take two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction conformation Crand1Position a to position b
Segment amino acid corresponding to dihedral angle replace barycenter conformation CcentroidSame position corresponding to dihedral angle, make simultaneously
Use Crand2Dihedral angle corresponding to the amino acid of segments of the upper position c to position d replaces barycenter conformation CcentroidSame position institute
Corresponding dihedral angle, then by gained CcentroidSegment is carried out to assemble to obtain variation conformation individual Cmutant；；
7) to the conformation C that makes a variationmutantIt executes crossover operation and generates test conformation Ctrial：
7.1) decimal rand3 is generated at random between zero and one；
If 7.2) rand3≤CR, integer rand4 is generated at random between 1 and L, utilize variation conformation CmutantIn piece
Section rand4 replaces target conformation CtargetIn corresponding segment, to generate test conformation CtrialIf rand3>CR, then Ctrial
It is directly equal to variation conformation Cmutant；
8) test conformation C is calculatedtrialEnergy value E (Ctrial), if E (Ctrial)-E(Ctarget) ＜ 0, show to test structure
As being better than target conformation, then conformation C is testedtrialReplace target conformation Ctarget；
9) judge whether to meet end condition, result is exported if meeting and exit, otherwise return to step 4).
Further, in the step 9), step 6) -8 has been carried out to each conformation individual in population) after, iteration
Number G=G+1, end condition are that iterations G reaches preset maximum iteration in step 3).
The present invention technical concept be：First, according to the energy value of each conformation carry out ascending order arrangement, and calculate each conformation with
The average energy error amount of minimum energy conformation；Then, the lower conformation of selected part energy calculates barycenter conformation；Finally, root
Judge the search condition that algorithm is reached according to average energy error amount, test structure is generated to design different barycenter Mutation Strategies
As that is, if average energy error amount is more than the threshold value of setting, designing DE/rand-to-centroid/1 strategies and being become
It is different, the homologous segment in the conformation randomly selected is replaced by the Partial Fragment extracted in barycenter conformation and generates test conformation, it is no
DE/centroid/2 strategies are then designed into row variation, are replaced in barycenter conformation by the segment extracted in randomly selected conformation
Homologous segment generate test conformation, to improve algorithm search efficiency and precision of prediction.
Beneficial effects of the present invention are shown：Barycenter conformation is calculated according to the lower conformation of energy, and by extracting barycenter
The evolution information design barycenter Mutation Strategy of conformation generates test conformation, to improve precision of prediction；Secondly, according to average energy
Error amount judges the search condition that algorithm is reached, to which design is suitble to the barycenter Mutation Strategy of corresponding states to generate test structure
As achieving the effect that improve algorithm search efficiency.
Description of the drawings
Fig. 1 is the flow chart of Advances in protein structure prediction in the present invention.
Fig. 2 is the conformation update schematic diagram when prediction technique in the present invention predicts protein 4ICB.
Fig. 3 is the conformation distribution map obtained when the prediction technique in the present invention predicts protein 4ICB.
Fig. 4 is the three-dimensional structure that the prediction technique in the present invention predicts protein 4ICB.
Specific implementation mode
The invention will be further described below in conjunction with the accompanying drawings.
Referring to Fig.1 and Fig. 4, one kind being based on barycenter Mutation Strategy differential evolution Advances in protein structure prediction, including following
Step：
1) protein force field model, i.e. energy function E (X) are chosen；
2) list entries information is given；
3) it initializes：Population Size NP is set, factor CR is intersected, maximum iteration generates initial structure by list entries
As populationAnd iterations G=0 is initialized,
In, N representation dimensions,Indicate i-th of conformation CiN-dimensional element；
4) the energy function value E (C of current each conformation of population are calculatedi), i=1,2 ..., N, and according to each in current population
Conformation energy value carries out ascending order arrangement to each conformation；
5) remember the conformation C of minimum energy in current populationbest, and calculate the energy and C of other conformationsbestENERGY E
(Cbest) average energy errorIf iterations G=0, enables δmax=δ；
6) each conformation individual C being directed in populationi, i ∈ { 1,2,3 ..., NP } enable Ctarget=Ci, CtargetIndicate mesh
Conformation individual is marked, the lower Constellation information of energy in current population is extracted, following operation is executed and generates variation conformation Cmutant：
6.1) CT conformation before selection rankingWherein CT=
Rand (NP/3, NP/2), rand (NP/3, NP/2) indicate the random integers between NP/3 and NP/2,Indicate m-th of choosing
Take the N-dimensional element of conformation；
6.2) the barycenter conformation C of CT selected conformation is calculatedcentroid=(xcentroid,1,xcentroid,2,…,
xcentroid,N), wherein conformation CcentroidJth tie up elementJ=1,
2,…,N；
6.3) sequence length L is set, generates 4 integers randint1, randint2, randint3 at random between 1 and L
And randint4, wherein randint1 and randint2, randint3 and randint4 it is different, enable a=min
(randint1, randint2), b=max (randint1, randint2), c=min (randint3, randint4), d=
Max (randint3, randint4), wherein min indicate that the minimum value of two numbers, max is taken to indicate to take the maximum value of two numbers；
If 6.4) 0.5 δ of δ ＞max, then DE/rand-to-centroid/ strategies are designed into row variation：From current population
Randomly select two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction barycenter conformation Ccentroid
Dihedral angle corresponding to amino acid of the position a to the segment of position b replaces conformation Crand1Same position corresponding to dihedral angle,
Extract conformation C simultaneouslyrand2Dihedral angle corresponding to amino acid of the position c to the segment of position d replaces conformation Crand1Same position
Corresponding dihedral angle, then by gained Crand1Segment is carried out to assemble to obtain variation conformation individual Cmutant；
If 6.5) δ of δ≤0.5max, then DE/centroid/2 strategies are designed into row variation：It is selected at random from current population
Take two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction conformation Crand1Position a to position b
Segment amino acid corresponding to dihedral angle replace barycenter conformation CcentroidSame position corresponding to dihedral angle, make simultaneously
Use Crand2Dihedral angle corresponding to the amino acid of segments of the upper position c to position d replaces barycenter conformation CcentroidSame position institute
Corresponding dihedral angle, then by gained CcentroidSegment is carried out to assemble to obtain variation conformation individual Cmutant；；
7) in order to improve the diversity of population, to the conformation C that makes a variationmutantIt executes crossover operation and generates test conformation Ctrial：
7.1) decimal rand3 is generated at random between zero and one；
If 7.2) rand3≤CR, integer rand4 is generated at random between 1 and L, utilize variation conformation CmutantIn piece
Section rand4 replaces target conformation CtargetIn corresponding segment, to generate test conformation CtrialIf rand3>CR, then Ctrial
It is directly equal to variation conformation Cmutant；
8) test conformation C is calculatedtrialEnergy value E (Ctrial), if E (Ctrial)-E(Ctarget) ＜ 0, show to test structure
As being better than target conformation, then conformation C is testedtrialReplace target conformation Ctarget；
9) judge whether to meet end condition, result is exported if meeting and exit, otherwise return to step 4).
In the step 9), step 6) -8 has been carried out to each conformation individual in population) after, iterations G=G
+ 1, end condition is that iterations G reaches preset maximum iteration in step 3)
The α unfolded proteins 4ICB that the present embodiment sequence length is 76 is embodiment, a kind of based on barycenter Mutation Strategy
Differential evolution Advances in protein structure prediction, wherein comprising the steps of：
1) Rosetta score3 force field models, i.e. energy function E (X) are chosen；
2) sequence information of input albumen matter 4ICB；
3) it initializes：Population Size NP=50 is set, factor CR=0.5, maximum iteration 10000, by defeated are intersected
Enter sequence and generates initial configurations population And it initializes and changes
Generation number G=0, wherein N representation dimensions,Indicate i-th of conformation CiN-dimensional element；
4) the energy function value E (C of current each conformation of population are calculatedi), i=1,2 ..., N, and according to each in current population
Conformation energy value carries out ascending order arrangement to each conformation；
5) remember the conformation C of minimum energy in current populationbest, and calculate the energy and C of other conformationsbestENERGY E
(Cbest) average energy errorIf iterations G=0, enables δmax=δ；
6) each conformation individual C being directed in populationi, i ∈ { 1,2,3 ..., NP } enable Ctarget=Ci, CtargetIndicate mesh
Conformation individual is marked, the lower Constellation information of energy in current population is extracted, following operation is executed and generates variation conformation Cmutant：
6.1) CT conformation before selection rankingWherein CT
=rand (NP/3, NP/2), rand (NP/3, NP/2) indicate the random integers between NP/3 and NP/2,It indicates m-th
Choose the N-dimensional element of conformation；
6.2) the barycenter conformation C of CT selected conformation is calculatedcentroid=(xcentroid,1,xcentroid,2,…,
xcentroid,N), wherein conformation CcentroidJth tie up elementJ=1,
2,…,N；
6.3) be arranged sequence length L=76, generated at random between 1 and L 4 integer randint1, randint2,
Randint3 and randint4, wherein randint1 and randint2, randint3 and randint4 are different, enable a=min
(randint1, randint2), b=max (randint1, randint2), c=min (randint3, randint4), d=
Max (randint3, randint4), wherein min indicate that the minimum value of two numbers, max is taken to indicate to take the maximum value of two numbers；
If 6.4) 0.5 δ of δ ＞max, then DE/rand-to-centroid/ strategies are designed into row variation：From current population
Randomly select two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction barycenter conformation Ccentroid
Dihedral angle corresponding to amino acid of the position a to the segment of position b replaces conformation Crand1Same position corresponding to dihedral angle,
Extract conformation C simultaneouslyrand2Dihedral angle corresponding to amino acid of the position c to the segment of position d replaces conformation Crand1Same position
Corresponding dihedral angle, then by gained Crand1Segment is carried out to assemble to obtain variation conformation individual Cmutant；
If 6.5) δ of δ≤0.5max, then DE/centroid/2 strategies are designed into row variation：It is selected at random from current population
Take two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction conformation Crand1Position a to position b
Segment amino acid corresponding to dihedral angle replace barycenter conformation CcentroidSame position corresponding to dihedral angle, make simultaneously
Use Crand2Dihedral angle corresponding to the amino acid of segments of the upper position c to position d replaces barycenter conformation CcentroidSame position institute
Corresponding dihedral angle, then by gained CcentroidSegment is carried out to assemble to obtain variation conformation individual Cmutant；；
7) in order to improve the diversity of population, to the conformation C that makes a variationmutantIt executes crossover operation and generates test conformation Ctrial：
7.1) decimal rand3 is generated at random between zero and one；
If 7.2) rand3≤CR, integer rand4 is generated at random between 1 and L, utilize variation conformation CmutantIn piece
Section rand4 replaces target conformation CtargetIn corresponding segment, to generate test conformation CtrialIf rand3>CR, then Ctrial
It is directly equal to variation conformation Cmutant；
8) test conformation C is calculatedtrialEnergy value E (Ctrial), if E (Ctrial)-E(Ctarget) ＜ 0, show to test structure
As being better than target conformation, then conformation C is testedtrialReplace target conformation Ctarget；
9) step 6) -8 has been carried out to each conformation individual in population) after, iterations G=G+1, if iteration time
Number G reaches maximum iteration 10000, then exports result and exit, otherwise return to step 4).
The α unfolded proteins 4ICB for being 76 using sequence length has obtained the protein as embodiment with above method
Nearly native state conformation, lowest mean square root deviation areAverage root-mean-square deviation isPredict obtained three-dimensional structure
As shown in Figure 4.
Described above is the excellent effect of optimization that one embodiment that the present invention provides shows, it is clear that the present invention is not
It is suitable only for above-described embodiment, and can be applied to the every field in Practical Project, while substantially smart without departing from the present invention
God and without departing from content involved by substantive content of the present invention under the premise of can do many variations to it and be implemented.
Claims (2)
1. a kind of differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy, it is characterised in that：The protein
Structure Prediction Methods include the following steps：
1) protein force field model, i.e. energy function E (X) are chosen；
2) list entries information is given；
3) it initializes：Population Size NP is set, factor CR is intersected, maximum iteration generates initial configurations kind by list entries
GroupAnd initialize iterations G=0, wherein N
Representation dimension,Indicate i-th of conformation CiN-dimensional element；
4) the energy function value E (C of current each conformation of population are calculatedi), i=1,2 ..., NP, and according to each conformation in current population
Energy value carries out ascending order arrangement to each conformation；
5) the conformation C of minimum energy in current population is found outbest, and calculate the energy and C of other conformationsbestENERGY E (Cbest)
Average energy errorIf iterations G=0, enables δmax=δ；
6) each conformation individual C being directed in populationi, i ∈ { 1,2,3 ..., NP } enable Ctarget=Ci, CtargetIndicate target structure
As individual, the lower Constellation information of energy in current population is extracted, following operation is executed and generates variation conformation Cmutant：
6.1) CT conformation before the lower ranking of energy is chosen in current population
Wherein CT=rand (NP/3, NP/2), rand (NP/3, NP/2) indicate the random integers between NP/3 and NP/2,It indicates
The N-dimensional element of m-th of selection conformation；
6.2) the barycenter conformation C of CT selected conformation is calculatedcentroid=(xcentroid,1,xcentroid,2,…,xcentroid,N),
Wherein, conformation CcentroidJth tie up element
6.3) be arranged sequence length L, generated at random between 1 and L 4 integers randint1, randint2, randint3 and
Randint4, wherein randint1 and randint2, randint3 and randint4 are different, enable a=min (randint1,
Randint2), b=max (randint1, randint2), c=min (randint3, randint4), d=max
(randint3, randint4), wherein min indicate that the minimum value of two numbers, max is taken to indicate to take the maximum value of two numbers；
If 6.4) 0.5 δ of δ ＞max, then DE/rand-to-centroid/ strategies are designed into row variation：It is random from current population
Choose two different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction barycenter conformation CcentroidPosition
Dihedral angle corresponding to amino acid of a to the segment of position b replaces conformation Crand1Same position corresponding to dihedral angle, simultaneously
Extract conformation Crand2Dihedral angle corresponding to amino acid of the position c to the segment of position d replaces conformation Crand1Same position institute is right
The dihedral angle answered, then by gained Crand1Segment is carried out to assemble to obtain variation conformation individual Cmutant；
If 6.5) δ of δ≤0.5max, then DE/centroid/2 strategies are designed into row variation：Two are randomly selected from current population
A different conformation Crand1And Crand2, wherein rand1 ≠ rand2 ∈ [1, NP], extraction conformation Crand1Pieces of the position a to position b
Dihedral angle corresponding to the amino acid of section replaces barycenter conformation CcentroidSame position corresponding to dihedral angle, use simultaneously
Crand2Dihedral angle corresponding to the amino acid of segments of the upper position c to position d replaces barycenter conformation CcentroidSame position institute is right
The dihedral angle answered, then by gained CcentroidSegment is carried out to assemble to obtain variation conformation individual Cmutant；；
7) to the conformation C that makes a variationmutantIt executes crossover operation and generates test conformation Ctrial：
7.1) decimal rand3 is generated at random between zero and one；
If 7.2) rand3≤CR, integer rand4 is generated at random between 1 and L, utilize variation conformation CmutantIn segment
Rand4 replaces target conformation CtargetIn corresponding segment, to generate test conformation CtrialIf rand3>CR, then CtrialDirectly
It connects equal to variation conformation Cmutant；
8) test conformation C is calculatedtrialEnergy value E (Ctrial), if E (Ctrial)-E(Ctarget) ＜ 0, show that test conformation is excellent
In target conformation, then conformation C is testedtrialReplace target conformation Ctarget；
9) judge whether to meet end condition, result is exported if meeting and exit, otherwise return to step 4).
2. a kind of double-deck differential evolution Advances in protein structure prediction based on barycenter Mutation Strategy as described in claim 1,
It is characterized in that：In the step 9), step 6) -8 has been carried out to each conformation individual in population) after, iterations G
=G+1, end condition are that iterations G reaches preset maximum iteration in step 3).
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| CN107066834B (en) * | 2017-03-23 | 2019-05-31 | 王晨彤 | A kind of protein structure ab initio prediction method based on particle swarm optimization algorithm |
| CN109509510B (en) * | 2018-07-12 | 2021-06-18 | 浙江工业大学 | Protein structure prediction method based on multi-population ensemble variation strategy |
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